Project Summary: The ultimate goal of project 2 is the discovery of the genes that drive prostate cancer pathogenesis. Since most of the risk variants discovered to date reside outside of known protein coding regions (i.e., intronic and intergenic), systematic approaches are required to reveal the connection between the risk allele and the gene that it influences. The primary hypotheses that we are comprehensively testing are that the risk regions harbor an as yet undiscovered transcript and/or that the risk regions are functional elements (e.g., promoters and enhancers) that influence gene expression. A range of complementary techniques is proposed that will thoroughly address these hypotheses. The prostate transcriptome will be sequenced to derive an unbiased census of coding and non-coding transcripts and alternative splicing. Functionally relevant elements within the prostate cancer risk loci regions will be annotated using the techniques of chromatin immunoprecipitation and DNase hypersensitivity. Finally, methods will be employed to functionally characterize each of the risk loci, including chromosome conformation capture to identify all other genomic regions that are interacting with the risk region, gene perturbation (e.g., knockdown and overexpression) experiments of candidate genes surrounding the risk regions, and evaluating associations between the risk alleles and transcript abundance across candidate genes. Understanding the biologic pathways driving prostate cancer provides a sound basis for rational intervention in disease prevention and treatment.